Added a SourceTracker tutorial rst file and image related to that tutorial
updated to use open-reference otu picking and core_diversity_analyses.py

need to make an udpate to qiime to use change from #741.
updated to use open reference otu picking and core_diversity_analyses.py
added check_id_map.py step
changed {} to None as default function parameters and more

It is advised not to use mutable object (such as {} and []) as default
parameters to avoid possible bugs. See
http://satyajit.ranjeev.in/2012/01/12/python--dangerous-default-value-as-argument.html
for details.

Also fixed a typo
Merge branch 'master' of github.com:qiime/qiime into sourcetracker_tutorial
Removed example output from help command in order to avoid confilicts with changes to the option list in future releases.
added text to clarify the description of the filter_otus_from_otu_table.py
Improved the description of adding columns to the mapping file.
made a few minor changes to clarify descriptions and fix grammer.
Fixing --input_fps option for count_seqs.py. Not finished (currently does not support filepath pattern expansions)
Now requires minimum version of R instead of exact match, see issue #624
added the print_qiime_config.py command to the tutorial.
Fixing ci_type and metrics option type of conditional_uncovered_probability.py
Fixing test_alpha_diversity.py in test_pycogent_backports
Merge branch 'master' of github.com:qiime/qiime into conditional_uncovered_prob
Changing import from pycogent_backports.option_parsis to qiime.util
Add descriptive error to add_alpha_to_mapping_file

The library function was changed to check for the existance of the
specified rarefaction depth; it will now raise an exception if a
non-existant depth is passed. This exception is now catched from the
script interface and displayed using option_parser.error.

The test suite was updated accordingly for this module.

An unnecessary type cast was also removed from the script interface.

This should fix #827
Add available depths to the exception message
Merge branch 'master' of github.com:qiime/qiime into conditional_uncovered_prob